Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1627 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0228665356 sf0228659487 2 28665356 1.90E-10 5.57E-06
vg0824712199 sf0824709485 8 24712199 2.41E-10 NA
vg0216000792 sf0215994922 2 16000792 3.33E-10 NA
vg0629827585 sf0629826587 6 29827585 3.59E-10 NA
vg0300707950 sf0300706948 3 707950 4.08E-10 NA
vg0514388692 sf0514331235 5 14388692 1.46E-09 3.51E-06
vg0426596087 sf0426410960 4 26596087 9.67E-09 NA